An immobile nucleic acid junction constructed from oligonucleotides

Abstract

Base-paired DNA duplexes involving oligonucleotide model systems have provided the major source of detailed structural and dynamic information about double helical structure1. Triple- and quadruple-branched ‘junction’ structures of DNA have a transient existence as intermediates in the replication or recombination of DNA molecules2–5 while cruciforms may be inducible by negatively supercoiling closed circular DNA6–11. However, it has not been possible to investigate these forms structurally at high resolution in short-chain molecules, where the junction will yield a significant component of the signal, because these naturally occurring intermediates are inherently unstable, due to internal sequence symmetry, which permits their resolution to double helices, via branchpoint migration12–15. We have recently proposed that migration can be eliminated to yield immobile junctions from oligonucleotides16–19 by combining sequence symmetry constraints with equilibrium calculations. We present here electrophoretic and UV optical absorbance experiments which indicate that four hexadecadeoxynucleotides (Fig. 1) indeed do form a stable tetrameric junction complex in solution.